Nate Parks wrote:

>  Does AFNI have an automated coregistration tool? 
>  I thought you could only do manual coreg in AFNI.

AFNI coregistration program is 3dvolreg.

See docs:

http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html

And if you are having trouble finding which AFNI program does what, you might like my "all afni helps on one page":

http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm

Graham